In this tutorial, we’re going to examine why full-genome assemblies can be useful in population genetic and phylogenetic studies. For practical reasons, we have to move away from salamanders (☹️), because the only chromosome-level reference genome is 32 Gb! Nobody wants to deal with that for a tutorial.

Instead, we’ll use some real data from the pygmy rabbit (Brachylagus idahoensis). This is a small, endangered species found in the western United States.


We generated 3RAD data for several individuals of this species, and we assembled them similar to how we earlier assembled Urspelerpes data for this course. Rather than start from these raw data, we’re going to map the final loci to the reference genome.